Two Stage Rocket
by Soon to be world renown Gracie
Summary: Sheppard and his team sans McKay but plus Dr.Z step through the wormhole to find a very different city than the one they left. Something's off about the whole thing. Just like a 2 stage rocket just when you think it's over, it explodes again.
1. Chapter 1

Sheppard yawned and stood next to the DHD with impatience. "Come on, you guys! I don't know about you, but after four days of complete boredom I'm ready for the excitement of one of Beckett's post-mission proddings."

Teyla arrived and stood next to him, "Dr. Zelenka, have you enjoyed this offworld mission?"

Dr. Zelenka trudged up followed by a bored looking Ronon. "Was fine. I am just glad that there was no need for this," he patted the pistol strapped to his hip cautiously.

Sheppard smiled and began to dial the address into the DHD, "Rodney's going to be so jealous that he missed out on four days of walking, story telling, alcohol, and MREs. How did you sneak that Rot-Gut anyway?"

Zelenka smiled as Sheppard sent through their IDC, "That is my secret."

Sheppard grinned in response and stepped through the gate—

—To have ten rifles pointed at his team's chests.

A young woman with deep mahogany hair, greenish eyes and a glare was standing calmly between them at the foot of the ramp, "Who are you?" Her voice had a slight accent but it seemed quite neutral—she was well aware that she was in control.

Sheppard looked back at his team in confusion. Ronon was eyeing the soldiers, his hand twitching near his pistol. Teyla had an eyebrow raised, looking the young woman up and down. Zelenka caught his look and shrugged—they were definantly in Atlantis. "I'm Colonel John Sheppard. This-."

Several of the P-90s cocked ominously but the girl made no move to stop any of the soldiers. "You lie," she said, "You can't be him. Colonel Sheppard died twenty years ago, along with his team."

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	2. Chapter 2

Disclaimer that I forgot in the first chapter: I don't own Stargate: Atlantis. Only the plot belongs to moi! Next part should be up soon! This chapter contains a flashback (and I just loooove flashbacks) so be forewarned.

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Sheppard's jaw dropped and Teyla's eyebrow almost left her face. "B-but," Zelenka started before switching to rapid Czech.

"Speak English, little man," Ronon growled.

Unable to find adequate English expletives to express his feelings, Zelenka shut his mouth.

Sheppard managed to get his brain working again and, with all the intelligence he could muster said, "A-wha-?"

The girl's brow furrowed in confusion as she raised the small radio in her hand to speak into it, "Uncle Carson, could you please come to the 'Gate room?"

"Uncle Carson?" Ronon turned to Teyla who shrugged, mimicking Zelenka's earlier motion.

"We'll find out if you are who you say you are."

A tense moment later an older man, easily in his mid-fifties entered and limped up to the girl, "Sammy? What's all-?" He stopped in mid-sentence, noticing the four in front of the 'gate.

'Sammy' frowned and Sheppard's jaw almost hit the floor. Teyla's eyebrows were completely gone along with all the color from Zelenka's face. Ronon just looked thoroughly confused.

"Uncle Carson? Are you OK?"

"Dr. Beckett?" Ronon mumbled from behind the three.

Carson seemed to regain his composure quickly enough, "Right, then. To the infirmary, the lot of you. Post mission checks." He moved out of the way to allow them to pass by the guards and as he did they lowered their weapons.

"Defiantly Dr. Beckett," Radek informed Ronon with a nod. Sheppard and Teyla brought up the end of their little troop behind Carson, Sammy, Radek and Ronon. Teyla turned to him and murmured conspiratorially, "Did you notice their clothing?"

Sheppard raised an eyebrow, "Carson looks the same-."

"I was not talking of Dr. Beckett. The girl wears fatigue pants and an Athosian top. Most of the children wore the same."

"Children?"

"Yes. In the 'gate room. Did you not notice them?"

"I was more focused on the ones with the guns."

She gave him an indecipherable look, "They were the ones with the guns."

They walked in silence for a beat. "I don't recognize any of these soldiers." They arrived in the infirmary and looked around with surprise.

"Forgive the mess," Carson said, "After a while, you just stop caring." He patted a bed and Sheppard hopped on, the other three following his lead, Sammy leaning against a close-by wall.

"Are you sure, Uncle Carson?" The girl asked, suspicion evident in her tone.

"Aye, lass. As sure as I'm standin' here," Carson replied.

"But, I mean, they're not… not…"

"I know, lass," he shook his head as he finished Sheppard's scan, "They're perfectly healthy. Still young. After twenty years…"

"Doc," Sheppard cut in, "it was only four days."

"Aye," Beckett asked with an amused smirk, "I suppose in four days I turned out like this?" He gestured to his gray hair and slightly wrinkled face.

"Well, I always said your worrying was having an adverse affect."

Expecting at least an exasperated sigh and a head shaking, at most an angry Scottish mumble, Sheppard was surprised when Beckett burst into laughter. He looked around that the stunned faces of his team and stopped at Sammy. She had tensed slightly, her head cocked to the side, a shocked expression evident on her face as she watched Carson laugh. Then, she grinned. John paused. He recognized that grin; but, from where?

"Excuse me," Teyla said hesitantly, "I am…very confused."

"Yeah," Sheppard nodded, "Sammy, is it? Where's Dr. Weir? What's happened?"

"Oh," a look of embarrassment and sadness flittered across her face, "I'm sorry. Mom died in childbirth."

"Mom?"

"Oh, I forgot my manners!" She smiled and offered her hand to Sheppard who was closest, "I'm Samantha. Samantha Zelenka. Colonel, Atlantis is yours."

Sheppard's head snapped to Zelenka who was sitting on the gurney, his mouth slightly open in shock. Sammy still stood with her hand out. John's head snapped back to Sammy, "Wait… Atlantis is mine?"

Ronon looked at the scene and grunted, "Perhaps you should explain everything. From the beginning."

"Sure. Uncle Carson?"

Dr. Beckett nodded, "They seem completely fine. Why don't you give them a run down while I do some detailed scans? Try to work out what's happened."

Sheppard sighed, "Alright. Let's hear it. Everything."

Sammy nodded, "Alright." She sat down on Beckett's newly vacated chair she had dragged to the middle of the group so she could see them all. "I was born some months after you all disappeared."

Sheppard interrupted, "Wait. OK. So, you're saying you're Elizabeth's daughter?"

"Yes," Sammy nodded.

"And you're Radek's, too?" Sheppard asked, pointing accusingly at the Czech.

"Yes."

"Wha-? How? Radek!" Sheppard practically whined, "Why didn't you say anything?"

Zelenka got defensive, "I had no idea! I don't remember-."

"Hey, excuse me!" Sammy blurted, raising a hand, "Listening to my story?"

"Sorry."

"Where was I? Oh. When I was born, mom died. Leaving Atlantis leaderless."

"Caldwell?"

She shook her head, "We lost contact with Earth and the Daedelas before I was born. On the last trip of the Daedelas they brought books, supplies, mail, and took back anyone who wanted to go."

"Who?"

"Kavenaugh. They wanted mom to go back but she refused. They left and we haven't heard anything since. We tried to contact them but," she shrugged, "Nothing. We try once a year to reach either the ship or Earth. Every Christmas. It's tradition."

_"Are you sure you won't come with us?" Colonel Caldwell asked a very pregnant Dr. Weir._

_She smiled the patented, disarming political smile, "I'm sure, Colonel. Good journey to you."_

_He took her hand, "It's going to be dangerous, Elizabeth. We can keep you safe on Earth. You're fighting a war. We're not." He inclined his head slightly. All was quiet for a moment before he let go of her hand, "What are you going to name it?"_

_Elizabeth shrugged and stared out at the ocean. He had led her out onto he balcony in one last-ditch effort to get her to return. Pegasus was no place for children, with Wraith running around and phantom planets just eating 'gates._

_Weir spoke, startling him, "I didn't get the chance to tell him, you know. Radek. I didn't get to tell him. They were only supposed to be gone four days—a simple milk run."_

_Caldwell nodded, no knowing what to say to make her feel better, "I thought you might feel that way so my crew got together and got you something." Elizabeth raised an eyebrow and he continued, "We brought every textbook we could fine. And lots of baby supplies." _

"_Why, Colonel. Keep that up and somebody might think you have a heart after all."_

_He raised an eyebrow and smirked slightly, "Don't get too comfortable. Your Lieutenant Cadman got together with my pilot and got her to hit up everybody and anybody for money so they could buy the stuff back on Earth." He sighed and rose to his full height, "Dr. Weir, good luck". He shook her hand, "I'm sure he's fine."_

_She smiled lightly, "Godspeed, Colonel. Keep Earth safe."  
_

"_Oh, I'm taking that pompous ass back with me. I figured that the kid would have to deal with McKay and Kavenaugh would be too much."_

_She smiled, "I'm sure he's going to tell everybody what a bad job I did."_

"_Hmm. I heard Hermiod was having some trouble with the airlock doors."_

_She laughed, "You should get going, Colonel." She watched him walk away. "You can come out now, Doctor."_

_Beckett emerged from the shadows. She looked at him for a moment before he shrugged, "He's not half bad. Now, come on. I'll buy you lunch. I think Laura's going through the supplies in the 'gate room."_

_She laughed again._

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	3. Chapter 3

"After Mom died," Sammy continued on, "The Athosians came back to Atlantis and Uncle Rodney took over the city."

"And yourself?" Teyla nudged when it became clear that the girl didn't want to share anymore. "With no parents who raised you?"

"Uncle Rodney, Uncle Carson and Aunt Laura raised me. Uncle Rodney brought me into his research and they taught me all they could. I studied astrophysics, some medicine, Jinto taught me self defense, Dr. Heightmeyer taught me English, I speak Ancient, and Egyptian, I've studied all the great politicians," she smiled, "Some of the greatest minds from Earth were here on Atlantis. I've had the best education in two galaxies."

"Yeah," Sheppard interrupted, "Where is Rodney?"

She replied quietly, "Dead. Six years ago. Surprise attack on the city." Her radio suddenly went off and she clicked it on, "Yes? ...Alright...Sure, I'll send him down and you can do your thing... Alright, yes... Ok... Out." She turned to the four. "You all have free run of the city. Dr. Zelenka, you are needed in the labs. I assume you know the way?"

Radek nodded and hopped off the table, walking out of the infirmary as in a trance.

"Colonel? If you'll come with me? There's much to show you."

"Colonel," Teyla jumped off her own table, "What do you wish us to do?" She motioned to herself, then Ronon.

"Uh. Go...sightsee..."

Teyla raised an eyebrow, obviously a favorite expression of hers, but Ronon put a hand on her shoulder, "Come on, Teyla, Let's go see your people."

"They're two levels down. I believe Jinto is in training with Sergeant Stackhouse at the moment," Sammy supplied helpfully.

Sheppard followed Sammy closely as she led him through a narrow passage that used to be a wide hallway, the lights flickering overhead.

"What happened to this place?" He asked as he maneuvered around a large piece of ceiling blocking his path.

"A lot of things happened after you left," she said easily.

He gave her a look as she gracefully navigated the blocked pathway, "I can see that."

They emerged from the darkened hallway into a larger, clearer passage. "Do you know where you are, yet?" She turned to him and smiled.

He frowned and looked around, "Hey, this is-."

She moved to a doorway and opened it, "Your quarters. I'm sorry if it's not what you remember. We've had some desperate times. We've had to ransack anyone's room that wasn't being occupied." She grew somber in a flash, "Even the dead's."

He let it slide and switched gears quickly, "Tell me who's in what position. I need to know."

"Oh. Of course. Uncle Carson is in charge of medical, Sgt. Stackhouse is in charge of military, science was being run by Dr. Simpson, but it's being turned over to Dr. Ze... my..." she stumbled, a frown creasing her brow.

"I got it. Can I ask you something?" He sat on the bed and motioned for her to do the same.

"Anything," she replied sincerely, gracefully lowering herself small frame next to his larger one.

"What the hell happened? I mean... This place is crazy. Beckett's normally obsessively shiny infirmary is a mess, the ceilings have decided to make the floor their new home, kids are shoving P90s in my face, underlings are in charge..." He paused and sighed, "Was it the Wraith?"

"The Wraith? No," she shook her head, "No. It was the Genii. They took us by surprise." She crossed her legs, "I suppose I should start at the beginning. I... I've been running Atlantis for six years now. Lorne has been helping. At first, it was odd. I wasn't in charge, but nobody quiet knew what o do. Lorne was in charge of everything but he didn't understand the civilian needs. The scientists came to me with questions about what Uncle Rodney was doing and if their research would tie in, and, eventually, Lorne did, too. By fifteen I was completely in charge of the city with even the military deferring to me."

"That's a lot of responsibility for a kid," he was genuinely impressed.

"I've been brokering trade agreements since I was ten, Colonel. With M7G-677."

"M7...wait. The planet with all the kids?"

"It didn't matter to them how young I was. I cut my teeth on that."

He nodded, "You still haven't told me what happened to the city."

She nodded, "I know."

_

* * *

She looked lovely–a perfect, angelic vision–as she walked down the aisle, garbed in ivory colored adornments, a beautiful gown crafted by Athosian and Atlantian women alike._

_He was as handsome as the day was long in a dress uniform with his family's tartan draped across his shoulder. A silly grin adorned his face as he watched her walk toward him._

_She reached the end of her walk and handed her bouquet of handpicked flowers–given to her by Athosian children when they found out that particular Earth tradition–to her maid-of-honor–Dr. Weir._

_Colonel Caldwell stood before them, a smile on his face, gleaming metals standing out on his dress uniform._

"_It is my privilege, as commander of the ship, to marry any two persons such as the couple you see before you now. Before the _Daedaeles _embarks for Earth, it is my honor to perform this ceremony._

_The ceremony went off without a hitch, rings were exchanged, and the very last of Dr. Zelenka's remaining hidden rot-gut was passed around for the toast of the first couple to be married on Atlantis._

"_Excuse me," Rodney clinked his tin cup with a fork until the crowd quieted down enough for him to speak, "As best man, I feel it is my duty to give a toast." He tactfully ignored the fact that the bride had cornered him one evening and told him that if he didn't give a nice speech he would be singing soprano from now on. "To the bride and groom. Two great friends, and great people. Without you, Atlantis would fall." Noting the uncomfortable silence at his faux-pas, and that the absence of their friends became more noticeable, he hurriedly added, "Laura, thank God you're out of my head." He raised his cup high, "To the Becketts."_

_Laughter sounded as people clunked the military issue tin cups in a toast to the new couple._

"_And," McKay broke in, "Even on this happy occasion, I feel we should remember those who could not be here with us to celebrate like I know they would've wanted to." He glanced over at the newlyweds and noticed them nodding slightly, giving him permission to continue, "To those we have lost. Sumner, Gaul, Markham, Grodin, Ford, Ronon, Teyla, Zelenka, Sheppard, just to name a few." He raised his cup once more, "To the lost."_

_The toasting was more somber the second time around. _


End file.
